US6461817B1 - Non-competitive co-amplification methods - Google Patents

Non-competitive co-amplification methods Download PDF

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US6461817B1
US6461817B1 US09/508,343 US50834300A US6461817B1 US 6461817 B1 US6461817 B1 US 6461817B1 US 50834300 A US50834300 A US 50834300A US 6461817 B1 US6461817 B1 US 6461817B1
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probes
amplification
sequence
assay
reaction
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David Alland
Fred R. Kramer
Amy Piatek
Sanjay Tyagi
Jacqueline Vet
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PAUL ROYALTY FUND LP
PHRI Properties Inc
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6851—Quantitative amplification

Definitions

  • This invention relates to amplification assays to detect nucleic-acid targets.
  • the target sequence may be RNA or DNA.
  • amplification of a target sequence we mean to include amplification of the target sequence itself and also amplification of a transcript thereof, as when an RNA target sequence is amplified by first creating a DNA transcript with reverse transcriptase and then amplifying the DNA transcript.
  • exposure amplification we mean an amplification reaction or reactions that generate products (“amplicons”) that include both plus strands and complementary minus strands.
  • control sequences, amplicons and probes we mean to include both plus and minus strands.
  • cross hybridization of a control sequence with a target sequence or to cross hybridization of two target sequences during amplification we are referring to hybridization of the plus strand of one to the minus strand of the other.
  • hybridization of a probe to a target sequence we mean to include hybridization of the probe to either the plus-strand or the minus strand of the target sequence itself or to an amplicon, that is a plus-strand copy or minus-strand copy of the target sequence.
  • PCR polymerase chain reaction
  • NASBA nucleic acid sequence-based amplification
  • TMA transcription-mediated amplification
  • 3 SR self-sustained sequence replication
  • SDA strand displacement amplification
  • RT-PCR DNA and RNA
  • PCR is used for detection even at the level of a single cell (in situ PCR).
  • Quantitative PCR assays are also well known. Quantitative PCR assays for DNA and RNA have been widely used to study disease processes (see, for example, Clementi et al., 1993).
  • One type of quantitative PCR assay involves simultaneously amplifying control molecules and samples containing (or suspected to contain) a target sequence. Receptacles containing known amounts of control molecule are thermally cycled with receptacles, most commonly tubes or wells or slides, containing the unknown amount of target. In addition to the pair of PCR primers for the target, a pair of PCR primers is required for each control molecule. Following amplification, the amounts of amplified products (amplicons) are compared. See generally Clementi el al., 1994 and Kahn et al., 1992. Partly due to variation in amplification efficiency among primers, only relative quantitation between samples is possible.
  • QC PCR quantitative-competitive PCR
  • a control molecule which is similar to but ultimately distinguishable from the target sequence competes with the target sequence for the same pair of primers.
  • the two products synthesized (amplicons) are distinguished, for example, by size using gel electrophoresis. See generally Wang et al., 1989 and Becker-Andre, 1991.
  • QC PCR has inherent disadvantages and limitations. Post-amplification manipulation is required. This complicates the assay, decreases throughput, increases labor, and risks contamination of untested samples by amplicon carryover.
  • Assay design is complicated by the need for a competitor-control that amplifies with an efficiency very close to that of the target unknown. For reasonable quantitation, most QC PCR assays are performed in multiple tubes containing serial dilutions, of the competitor-control, typically five-fold dilutions, but in some assays two-fold dilutions for better accuracy. Differences in amplification efficiency between the target and the competitor-control usually compel analysis during the exponential phase of amplification, because errors become too large during the subsequent linear phase. (Mullis and Faloona, 1987). Precision is limited, varying a minimum of fifty percent between parallel assays.
  • a more recently developed type of quantitative PCR assay has been called the 5′-nuclease assay and “real-time PCR.” See generally, Gibson et al., 1996; Heid et al., 1996; Gelfand et al., 1993; and Livak et al., 1996.
  • This method utilizes detector probes that are linear DNA sequences labeled with two different fluorescent dyes, for example, a reporter dye such as FAM and a quenching dye such as TAMRA.
  • a reporter dye such as FAM
  • TAMRA quenching dye
  • Commercial kits from the Applied Biosystems Division of The Perkin-Elmer Corporation are available under the trademark TaqManTM.
  • the quenching dye When not hybridized to target (original unknown or amplicon) the quenching dye partially quenches the reporter dye.
  • the probes hybridize to the target sequence, and during the extension step of the PCR cycle, the probes are cleaved by the 5′ ⁇ 3′ nucleolytic activity of DNA polymerase. Cleavage releases the reporter dye from the quenching dye, resulting in an increase in fluorescence. Fluorescence can be monitored throughout the PCR amplification.
  • molecular beacon possesses a stem-and-loop structure, has a higher signal-to-background ratio than linear probes and also has improved allele discrimination.
  • molecular beacon probes hybridize to the target sequence and fluoresce, but during the extension step of the PCR cycle, the probes leave the target and do not interfere with polymerization.
  • An aspect of this invention is nucleic acid hybridization assays that do not require post-amplification manipulation, that include at least two sequences which are subject to the same reaction kinetics, and that include homogenous detection utilizing interactively labeled hybridization probes.
  • Another aspect of this invention is quantitative, homogeneous PCR assays wherein the precision is significantly improved over the thirty-percent variability of real-time PCR.
  • Another aspect of this invention is homogenous nucleic acid hybridization assays, including especially PCR assays, to detect amounts of two co-amplifiable, cross hybridizable targets in a sample, either the relative amount of one to the other or absolute amounts of both, with high precision.
  • cross hybridize we mean that the amplicons of each sequence hybridize not only to themselves but also to amplicons of the other sequences. For such sequences, the amplifications of the sequences are linked; they follow the same reaction kinetics and act as a single amplicon. We refer to this as non-competitive amplification. It differs from competitive amplification, such as in QC PCR (wherein two sequences compete for a single set of primers and follow different reaction kinetics, and where one sequence may grow at the expense of the other). The difference is profound with respect to quantitation and relative quantitation in homogeneous detection assays in which tubes are not opened for further manipulation following amplification.
  • Detection in the assays of this invention utilizes what we refer to as “dual-labeled hybridization probes” by which we mean hybridization probes having at least two interactive labels, whose signal varies depending on whether the probe is hybridized to a strand or free-floating in a single-stranded conformation. Fluorescent labels are preferred and will be used to illustrate and explain such probes. Such probes are suitable for homogeneous assays, because separation of bound probes from unbound probes is not required, as is required when traditional fluorescently labeled probes not having interactive labels are used. As stated above, we are aware of two different types of dual-labeled hybridization probes.
  • the probe is a linear oligonucleotide complementary to a non-primer portion of a sequence to be amplified (that is, it hybridizes between the primers, for example, PCR primers).
  • the probe is labeled at two nucleotides removed from each other with a reporter dye such as FAM and a quenching dye such as TAMRA.
  • the quencher When the probe is not hybridized to a strand, the quencher partially quenches the fluorescence of the reporter.
  • the probe hybridizes to the target sequence, as during the annealing step of PCR, it sits in the path of the DNA polymerase that will generate a copy, as in the extension step of PCR.
  • the DNA polymerase cleaves the probe, thereby permanently severing the reporter from the quencher.
  • Such probes have a limited ability to “allele discriminate,” by which we mean to distinguish between two sequences that differ by as little as a single nucleotide.
  • a second type of dual-labeled hybridization probe useful in assays according to this invention is a hairpin probe in which a probe sequence is a loop and flanking arm sequences form a double-stranded stem.
  • Each arm contains one of the at least two interactive labels, typically a fluorophore and a quencher.
  • Fluorescently labeled molecular beacons undergo a fluorogenic conformational change when they hybridize to their target.
  • a fluorescent moiety is covalently linked to the end of one arm and a quenching moiety is covalently linked to the end of the other arm.
  • the stem keeps these two moieties in close proximity to each other, causing the fluorescence of the fluorophore to be quenched by energy transfer.
  • the quencher is a non-fluorescent chromophore that emits the energy that it receives from the fluorophore as heat, fluorescence does not occur.
  • the probe encounters a target molecule, it forms a probe-target hybrid that is longer and more stable than the stem hybrid.
  • the rigidity and length of the probe-target hybrid precludes the simultaneous existence of the stem hybrid. Consequently, the molecular beacon undergoes a spontaneous conformational reorganization that forces the stem hybrid to dissociate and the fluorophore and the quencher to move away from each other, restoring fluorescence. Fluorescence increases as much as 900-fold when these probes bind to their target.
  • molecular beacons Various label pairs may be used, including among others the fluorophore EDANS and the quencher DABCYL. These probes, called “molecular beacons”, and their preparation and use in homogenous, real-time PCR assays are described in Tyagi and Kramer, 1996, and in Tyagi et al., 1996, each of which is incorporated herein in its entirety. The ability of a molecular beacon probe containing a probe section 15 nucleotides long flanked by complementary arms, each 5 nucleotides long, to effectively discriminate between targets differing by a single nucleotide is described.
  • molecular beacon probes for use as dual-labeled probes in assays according to this invention. Specifically we prefer fluorescently labeled molecular beacons having a probe sequence 7-25 nucleotides in length and flanking arm sequences 3-8 nucleotides in length.
  • an assay utilizing non-competitive amplification of a target sequence is a quantitative assay for an unknown amount of a target sequence.
  • a co-amplifier DNA strand which will cross hybridize with the target sequence is utilized in known amount. We sometimes refer to this as a control molecule.
  • a probe specific for the target sequence and a probe specific for the co-amplifier are used.
  • Preferred probes are fluorescer/quencher-labeled molecular beacon probes (Tyagi and Kramer (1996)) which are capable of discriminating against a single base-pair mismatch. With these probes, the control molecule may be identical to the target sequence except at one nucleotide.
  • dual-labeled probes whose signal is a function of the amount of target (original target sequence or amplicon), such as TaqManTM probes described above, can also be used. In many instances a series of PCR amplification reactions containing a dilution series of the control molecule DNA will be used.
  • the ratio of the target sequence to the control molecule is constant throughout the PCR reaction, including in the linear phase.
  • the ratio can be determined at any cycle in which the fluorescences of both probes are above the background level. More preferably, the ratio can be determined at many cycles and averaged to provide an extremely accurate quantitation. Persons in the art will understand how to calculate the ratios.
  • probes can be employed, for example: a probe specific for the control (preferably complementary to a portion of the control sequence that differs by at least one nucleotide, preferably one nucleotide, from the corresponding portion of the target sequence of the unknown) and a probe specific for both the unknown and the control; a probe specific for the unknown and a probe specific for both the unknown and the control; a probe specific for the control and a probe specific for the unknown; and a probe specific for the control, a probe specific for the unknown and a third probe specific for both the control and the unknown (obviously complementary to a sequence that occurs in both the control and the unknown).
  • a probe specific for the control preferably complementary to a portion of the control sequence that differs by at least one nucleotide, preferably one nucleotide, from the corresponding portion of the target sequence of the unknown
  • a probe specific for both the unknown and the control a probe specific for the unknown and a probe specific for both the unknown and the control
  • three probes one specific for the unknown target sequence, one specific for the control, and one specific for both, that is, designed to hybridize equally to both the target and the control.
  • Use of three probes provides additional data and an internal control.
  • An instrument such as the ABI PRISM 7700, described above, can be programmed to make computations automatically. However, the method is so accurate that a single reading during, or at the end of, the PCR amplification can be used.
  • non-competitive PCR assays is an assay to detect the ratio of two closely related target sequences, such as alleles or mutants, for example, drug-resistant mutant pathogens.
  • Amplicons containing genetic alleles differing by a single nucleotide and amplicons containing drug-resistant mutants differing from a wild-type pathogen, for example bacterium or virus, by a single nucleotide will cross hybridize as required for non-competitive amplification.
  • the ratio of the progeny amplicons derived from the first unknown to progeny amplicons derived from the second unknown remains constant throughout the amplification, including the linear phase.
  • this embodiment can be precisely quantitative by using a control in a known amount.
  • FIG. 1 is a line graph showing the PCR amplification kinetics of a Mycobacterium tuberculosis strain M235 rpo B gene sequence present at a different concentration, in each reaction tube, relative to that of an rpo B gene sequence from M. tuberculosis strain J24.
  • the rpo B gene sequences from the 2 strains differ by a single nucleotide at position 561.
  • FIG. 2 is a line graph from an experiment carried out under the same conditions as that shown on FIG. 1, except that five-fold higher concentrations of the PCR primers were used.
  • FIG. 3 is a line graph showing the theoretical kinetics of amplification in three individual PCR reactions containing different numbers of template molecules.
  • FIG. 4 is a line graph showing the theoretical kinetics of amplification in a single PCR reaction containing the same number of template molecules as in all three PCR reactions depicted in FIG. 3 .
  • amplification of at least two closely related, cross hybridizing molecules occurs as a single amplicon with a single set of kinetics.
  • the individual amplifications are linked.
  • Two, three, four or five molecules can take part in a single PCR reaction, for example.
  • the fraction of the amplicons derived from each parent molecule remains constant throughout the amplification.
  • eff is the efficiency of amplification (effC being the efficiency of amplification of the control molecule and effU being the efficiency of amplification of the unknown), and
  • n is the number of PCR cycles (adapted from Clementi et al., 1994).
  • Co is the initial concentration of co-amplifier (which may be a control, an allele or a mutant, for example) and
  • C is the final concentration of the co-amplifier.
  • quantitation includes use of a factor k to correct for the difference.
  • k remains constant throughout a PCR amplification.
  • the relationship can be used in several ways. When u is the measured fluorescence of a molecular beacon that is specific for an unknown and n is the measured fluorescence of a molecular beacon specific for a co-amplifier,
  • M. tuberculosis strains M235 and J24 have identical DNA rpo B gene sequences except for a single G to T nucleotide substitution at codon 516.
  • a molecular beacon specific for the M235 rpo B sequence was constructed. This molecular beacon was found only to fluoresce in the presence of its appropriate target.
  • Eight PCR reactions using a primer pair which would amplify both M235 and J24 molecules were performed. The total amount of DNA in each tube was kept constant, but contained a different ratio of M235 and J24 DNA. Each reaction tube contained identical amounts of PCR reaction mixture and the molecular beacon specific to M235 rpo B.
  • Tube 1 contained 10 ng of M235
  • tube 2 contained 9.9 ng of M235 and 0.1 ng of J24
  • tube 3 contained 9 ng of M235 and 1 ng of J24
  • tube 4 contained 5 ng of each strain
  • tube 5 contained 1 ng of M235 and 9 ng of J24
  • tube 6 contained 0.1 ng of M235 and 9.9 ng of J24
  • tube 7 contained 10 ng of J24
  • tube 8 contained no chromosomal DNA and served as a molecular beacon only control.
  • the molecular beacon specific to M235 generated a series of fluorescent curves. Data obtained with tubes 2-8 are shown in FIG. 1 .
  • the decrease in M235 fluorescence may be partly explained if J24 DNA, which was also present in the PCR reaction, acted as a competitor for primers and other reagents. If two amplicons share primers in QC PCR, when the more abundant species reaches the plateau phase, amplification of the minority species is forced to plateau as well, due to exhaustion of shared primers. However, such competition should also increase the M235 cycle threshold. In the current experiment, the cycle thresholds for all samples were apparently the same but were decreased relative to that predicted by DNA concentration.
  • FIG. 2 shows data obtained from an experiment carried out as described for that shown in FIG. 1, except that a five-fold higher concentration of primers was used. Comparison of FIGS.
  • FIGS. 3 and FIG. 4 show idealized PCR reactions.
  • the top curve demonstrates PCR amplification starting with ten molecules.
  • the molecules amplify exponentially for four cycles, increase linearly for two cycles, then enter a lag phase ultimately ending in a plateau.
  • the middle and bottom curves show how a PCR reaction with the same kinetics would appear if independent reactions were begun with one half (middle curve) or one fifth (bottom curve) the number of target molecules (i.e., five molecules and two molecules, respectively).
  • Each PCR reaction is independent.
  • the model presented in FIG. 4 illustrates how the identical number of molecules would amplify if they were part of the same PCR reaction.
  • the top curve of FIG. 4 shows the amplification of ten molecules which amplify exponentially for four cycles, linearly for two cycles, then enter a lag phase, ending in a plateau. In this case, however, all curves represent the same PCR reactions.
  • the middle and bottom curves show how the same amplification would appear if only one half or one fifth of the molecules were visualized.
  • the linear phase starts after four cycles due to the limiting effect of primers and template reannealing.
  • the middle and bottom curves the linear phase is also entered after four cycles because every identical molecule in the PCR reaction is under the same constraints.
  • the ratio of the progeny amplicons derived from the starting subset represented in each curve to the total number of amplicons remains the same at every stage of the PCR, and the curves no longer rise in parallel. For example, one half of the molecules at the start of the reaction will amplify to produce one half of the molecules present at each stage of the reaction. The same data would be produced if three molecular beacons could be constructed so that one could visualize all of the molecules (top curve), one could visualize one half of the molecules (middle curve), and one could visualize one fifth of the molecules (bottom curve).
  • a striking aspect of FIG. 4 is that all linear phases of the PCR reaction extrapolate to a single point (as shown in this case by the lines intersecting at cycle number 2). This phenomenon must occur whenever linked reactions are plotted by molecular number (fluorescence) and PCR cycle.
  • Molecular beacons made with different fluorophores but constructed to hybridize with the same PCR amplicon can be used simultaneously in the same tube of a PCR reaction, and the ratio of their fluorescence is constant. This ratio does not change at any point in the PCR reaction (exponential or linear) and does not vary with subsequent assays or with different initial concentrations of template, as long as the same mixture of multiple molecular beacons is used.
  • Two molecular beacons were constructed, each designed to hybridize to different sequences in a 134 base pair amplicon of the M. tuberculosis rpo B gene.
  • One molecular beacon was labeled with fluorescein; the other was labeled with Texas red.
  • Reactions were carried out in five different tubes, each containing identical amounts of both molecular beacons in PCR reaction buffer, but different amounts of chromosomal M. tuberculosis DNA strain M235.
  • PCR reactions were performed for 50 cycles. The fluorescence spectra of each molecular beacon was simultaneously measured throughout the PCR reaction. Each molecular beacon generates different amounts of fluorescence but the fluorescent curves rise in parallel through the course of the PCR reaction.
  • a ratio of fluorescence of each molecular beacon can be calculated at a given PCR cycle. This ratio remains constant at any cycle number up to the 50 cycles performed. The fluorescent ratio remains identical when two different experiments are compared. This demonstrates that for a mixture of two molecular beacons which hybridize to the same target, a fluorescence ratio can be derived. This ratio can be combined with a measure of the fluorescence of one molecular beacon to calculate the fluorescence of the second molecular beacon.

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